Analysis of Genomic DNA Methylation Modification of Walnut by Methylation-sensitive Amplification Polymorphism

ZHOU Bei-bei; WEN Ming; MA Qing-guo; PEI Dong

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Analysis of Genomic DNA Methylation Modification of Walnut by Methylation-sensitive Amplification Polymorphism

1.
Research Institute of Forestry, Chinese Academy of Forestry, State Key Laboratory of Tree Genetics and Breeding, Beijing 100091, China
2.
Forestry Bureau of Liangshan Prefecture, Liangshan 615500, Sichuan, China

Received Date: 2013-12-22

Abstract

Taking the mature leaves of the walnut variety ‘Zhongningqiang’ to analyze the level and patterns of DNA methylation modification loci on the whole genome of walnut by modified MSAP (methylation-sensitive amplification polymorphism). By using 20 pairs of MSAP selective primers, a total of 1 060 legible and repeatable amplified DNA bands was detected, and 53 bands were observed after amplification with each primer pair in average. Of which, 241 bands at ‘CCGG/GGCC’ loci, detected among all the amplified loci, were DNA methylated loci, with 22.73% of methylated modification in genome of walnut. Ten methylated DNA sequences were isolated and sequenced by extraction of the methylated loci. The results of BLASTn comparison showed that the DNA methylated modification phenomenon existed in multiple types of DNA sequence. This research, on methylation loci of genomic-wide DNA in walnut, could provide references for the subsequent epigenetics research of walnut, as well as MSAP analysis of other woody plants.
- Juglans regia,
- methylation-sensitive amplification polymorphism,
- DNA methylation,
- epigenetic

References

[1]	Fjellstrom R G, Parfitt D E. RFLP inheritance and linkage in walnut[J]. Theoretical and Applied Genetics, 1994, 89(6): 665-670.
[2]	Chakrabarty D, Gupta V N, Datta S K. Varietal identification and assessment of genetic relationships in Hippeastrum using RAPD markers[J]. Plant Biotechnology Reports, 2007, 1(4): 211-217.
[3]	Bayazit S, Kazan K, Gülbitti S, et al. AFLP analysis of genetic diversity in low chill requiring walnut (Juglans regia L.) genotypes from Hatay, Turkey[J]. Scientia Horticulturae, 2007, 111(4): 394-398.
[4]	周贝贝, 马庆国, 王滑, 等. 核桃亲子鉴定方法的建立[J]. 中国农业科学,2011,44(20): 4258-4264.
[5]	Wang H, Pei D, Gu R, et al.Genetic diversity and structure of walnut populations in central and southwestern China revealed by microsatellite markers[J]. Journal of the American Society for Horticultural Science. 2008, 133(2): 197-203.
[6]	Reyna-Lopez G E, Simpson J, Ruiz-Herrera J. Differences in DNA methylation patterns are detectable during the dimorphic transition of fungi by amplification of restriction polymorphisms[J]. Molecular and General Genetics MGG, 1997, 253(6): 703-710.
[7]	Vos P, Hogers R, Bleeker M, et al. AFLP: a new technique for DNA fingerprinting[J]. Nucleic acids research,1995, 23(21): 4407-4414.
[8]	郭广平, 顾小平, 袁金玲, 等. 不同生理年龄毛竹DNA甲基化的MSAP分析[J]. 遗传,2011,33(7): 134-140.
[9]	洪柳, 邓秀新. 应用 MSAP 技术对脐橙品种进行 DNA 甲基化分析[J]. 中国农业科学,2005,38(11): 2301-2307.
[10]	Li X, Xu M, Korban S S. DNA methylation profiles differ between field-and in vitro-grown leaves of apple[J]. Journal of Plant Physiology,2002, 159(11): 1229-1234.
[11]	Zhang M, Xu C, von Wettstein D, et al. Tissue-specific differences in cytosine methylation and their association with differential gene expression in sorghum[J]. Plant physiology,2011, 156(4): 1955-1966.
[12]	Li A, Hu B, Xue Z, et al. DNA methylation in genomes of several annual herbaceous and woody perennial plants of varying ploidy as detected by MSAP[J]. Plant Molecular Biology Reporter, 2011, 29(4): 784-793.
[13]	Cao D, Gao X, Liu J, et al. Methylation sensitive amplified polymorphism (MSAP) reveals that alkali stress triggers more DNA hypomethylation levels in cotton (Gossypium hirsutum L.) roots than salt stress[J]. African Journal of Biotechnology, 2011, 10(82): 18971-18980.
[14]	Portis E, Acquadro A, Comino C, et al. Analysis of DNA methylation during germination of pepper (Capsicum annuum L.) seeds using methylation-sensitive amplification polymorphism (MSAP)[J]. Plant Science, 2004, 166(1): 169-178.
[15]	周贝贝, 陈凌娜, 王伟, 等. 适合MSAP分析的核桃子叶DNA提取方法研究[J]. 林业科学研究,2014,27(1):128-132.
[16]	Peraza-Echeverria S, Herrera-Valencia V A, Kay A J. Detection of DNA methylation changes in micropropagated banana plants using methylation-sensitive amplification polymorphism (MSAP)[J]. Plant Science,2001, 161(2): 359-367.
[17]	Ma Q, Zhang J, Pei D. Genetic Analysis of Walnut Cultivars in China Using Fluorescent Amplified Fragment Length Polymorphism[J]. Journal of the American Society for Horticultural Science, 2011, 136(6): 422-428.
[18]	Zhang M S, Yan H Y, Zhao N, et al. Endosperm-specific hypomethylation, and meiotic inheritance and variation of DNA methylation level and pattern in sorghum (Sorghum bicolor L.) inter-strain hybrids[J]. Theoretical and Applied Genetics, 2007, 115(2): 195-207.
[19]	洪舟, 施季森, 郑仁华, 等. 杉木亲本自交系及其杂交种 DNA 甲基化和表观遗传变异[J]. 分子植物育种,2009,7(3): 591-598.
[20]	Greenwood M S, Hopper C A, Hutchison K W. Maturation in larch I. Effect of age on shoot growth, foliar characteristics, and DNA methylation[J]. Plant physiology,1989, 90(2): 406-412.
[21]	张勇, 邓科君, 张韬, 等. 黑麦基因组 DNA 甲基化修饰位点的 MSAP 分析[J]. 麦类作物学报,2009,29(4): 559-564.
[22]	Finnegan E J, Peacock W J, Dennis E S. Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development[J]. Proceedings of the National Academy of Sciences, 1996, 93(16): 8449-8454.

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通讯作者: 陈斌, bchen63@163.com

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沈阳化工大学材料科学与工程学院沈阳 110142

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Analysis of Genomic DNA Methylation Modification of Walnut by Methylation-sensitive Amplification Polymorphism

1. Research Institute of Forestry, Chinese Academy of Forestry, State Key Laboratory of Tree Genetics and Breeding, Beijing 100091, China

2. Forestry Bureau of Liangshan Prefecture, Liangshan 615500, Sichuan, China

Received Date: 2013-12-22

Abstract: Taking the mature leaves of the walnut variety ‘Zhongningqiang’ to analyze the level and patterns of DNA methylation modification loci on the whole genome of walnut by modified MSAP (methylation-sensitive amplification polymorphism). By using 20 pairs of MSAP selective primers, a total of 1 060 legible and repeatable amplified DNA bands was detected, and 53 bands were observed after amplification with each primer pair in average. Of which, 241 bands at ‘CCGG/GGCC’ loci, detected among all the amplified loci, were DNA methylated loci, with 22.73% of methylated modification in genome of walnut. Ten methylated DNA sequences were isolated and sequenced by extraction of the methylated loci. The results of BLASTn comparison showed that the DNA methylated modification phenomenon existed in multiple types of DNA sequence. This research, on methylation loci of genomic-wide DNA in walnut, could provide references for the subsequent epigenetics research of walnut, as well as MSAP analysis of other woody plants.

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Reference (22)

[1]	Fjellstrom R G, Parfitt D E. RFLP inheritance and linkage in walnut[J]. Theoretical and Applied Genetics, 1994, 89(6): 665-670.
[2]	Chakrabarty D, Gupta V N, Datta S K. Varietal identification and assessment of genetic relationships in Hippeastrum using RAPD markers[J]. Plant Biotechnology Reports, 2007, 1(4): 211-217.
[3]	Bayazit S, Kazan K, Gülbitti S, et al. AFLP analysis of genetic diversity in low chill requiring walnut (Juglans regia L.) genotypes from Hatay, Turkey[J]. Scientia Horticulturae, 2007, 111(4): 394-398.
[4]	周贝贝, 马庆国, 王滑, 等. 核桃亲子鉴定方法的建立[J]. 中国农业科学,2011,44(20): 4258-4264.
[5]	Wang H, Pei D, Gu R, et al.Genetic diversity and structure of walnut populations in central and southwestern China revealed by microsatellite markers[J]. Journal of the American Society for Horticultural Science. 2008, 133(2): 197-203.
[6]	Reyna-Lopez G E, Simpson J, Ruiz-Herrera J. Differences in DNA methylation patterns are detectable during the dimorphic transition of fungi by amplification of restriction polymorphisms[J]. Molecular and General Genetics MGG, 1997, 253(6): 703-710.
[7]	Vos P, Hogers R, Bleeker M, et al. AFLP: a new technique for DNA fingerprinting[J]. Nucleic acids research,1995, 23(21): 4407-4414.
[8]	郭广平, 顾小平, 袁金玲, 等. 不同生理年龄毛竹DNA甲基化的MSAP分析[J]. 遗传,2011,33(7): 134-140.
[9]	洪柳, 邓秀新. 应用 MSAP 技术对脐橙品种进行 DNA 甲基化分析[J]. 中国农业科学,2005,38(11): 2301-2307.
[10]	Li X, Xu M, Korban S S. DNA methylation profiles differ between field-and in vitro-grown leaves of apple[J]. Journal of Plant Physiology,2002, 159(11): 1229-1234.
[11]	Zhang M, Xu C, von Wettstein D, et al. Tissue-specific differences in cytosine methylation and their association with differential gene expression in sorghum[J]. Plant physiology,2011, 156(4): 1955-1966.
[12]	Li A, Hu B, Xue Z, et al. DNA methylation in genomes of several annual herbaceous and woody perennial plants of varying ploidy as detected by MSAP[J]. Plant Molecular Biology Reporter, 2011, 29(4): 784-793.
[13]	Cao D, Gao X, Liu J, et al. Methylation sensitive amplified polymorphism (MSAP) reveals that alkali stress triggers more DNA hypomethylation levels in cotton (Gossypium hirsutum L.) roots than salt stress[J]. African Journal of Biotechnology, 2011, 10(82): 18971-18980.
[14]	Portis E, Acquadro A, Comino C, et al. Analysis of DNA methylation during germination of pepper (Capsicum annuum L.) seeds using methylation-sensitive amplification polymorphism (MSAP)[J]. Plant Science, 2004, 166(1): 169-178.
[15]	周贝贝, 陈凌娜, 王伟, 等. 适合MSAP分析的核桃子叶DNA提取方法研究[J]. 林业科学研究,2014,27(1):128-132.
[16]	Peraza-Echeverria S, Herrera-Valencia V A, Kay A J. Detection of DNA methylation changes in micropropagated banana plants using methylation-sensitive amplification polymorphism (MSAP)[J]. Plant Science,2001, 161(2): 359-367.
[17]	Ma Q, Zhang J, Pei D. Genetic Analysis of Walnut Cultivars in China Using Fluorescent Amplified Fragment Length Polymorphism[J]. Journal of the American Society for Horticultural Science, 2011, 136(6): 422-428.
[18]	Zhang M S, Yan H Y, Zhao N, et al. Endosperm-specific hypomethylation, and meiotic inheritance and variation of DNA methylation level and pattern in sorghum (Sorghum bicolor L.) inter-strain hybrids[J]. Theoretical and Applied Genetics, 2007, 115(2): 195-207.
[19]	洪舟, 施季森, 郑仁华, 等. 杉木亲本自交系及其杂交种 DNA 甲基化和表观遗传变异[J]. 分子植物育种,2009,7(3): 591-598.
[20]	Greenwood M S, Hopper C A, Hutchison K W. Maturation in larch I. Effect of age on shoot growth, foliar characteristics, and DNA methylation[J]. Plant physiology,1989, 90(2): 406-412.
[21]	张勇, 邓科君, 张韬, 等. 黑麦基因组 DNA 甲基化修饰位点的 MSAP 分析[J]. 麦类作物学报,2009,29(4): 559-564.
[22]	Finnegan E J, Peacock W J, Dennis E S. Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development[J]. Proceedings of the National Academy of Sciences, 1996, 93(16): 8449-8454.

Analysis of Genomic DNA Methylation Modification of Walnut by Methylation-sensitive Amplification Polymorphism

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通讯作者: 陈斌, bchen63@163.com

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Analysis of Genomic DNA Methylation Modification of Walnut by Methylation-sensitive Amplification Polymorphism

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